4.2 Transcription, Translation, and the Genetic Code

The Central Dogma in One Sentence

Genetic information flows DNA -> RNA -> protein, with transcription producing the messenger RNA (mRNA) and translation reading three-nucleotide codons to assemble a polypeptide. Praxis questions consistently test where each step happens, which enzymes are required, and what signals start and stop the process.

Transcription

Transcription synthesizes RNA from a DNA template. In eukaryotes it occurs in the nucleus; in prokaryotes it occurs in the cytoplasm and can be coupled directly to translation.

Key Players

• RNA polymerase reads the DNA template strand 3' to 5' and builds the RNA transcript 5' to 3'. Unlike DNA polymerase, it does not need a primer.
• The promoter is a DNA sequence upstream of the gene that recruits RNA polymerase. In prokaryotes, the -10 (Pribnow) box and -35 box are common promoter elements. In eukaryotes, the TATA box (about -25) helps position RNA polymerase II.
• The terminator is a downstream sequence that signals the end of transcription.
• The DNA strand that matches the mRNA sequence (with T -> U) is the coding strand (also called the sense strand). The opposite, complementary strand is the template strand.

Three Stages

1. Initiation - RNA polymerase binds the promoter (with sigma factor in prokaryotes; with general transcription factors in eukaryotes) and unwinds DNA.
2. Elongation - RNA polymerase walks along the template strand, adding ribonucleotides complementary to the template.
3. Termination - In bacteria, a hairpin loop (Rho-independent) or Rho protein causes release. In eukaryotes, polyadenylation signals trigger cleavage.

Eukaryotic mRNA Processing

Primary transcripts (pre-mRNA) are processed before export to the cytoplasm.

Alternative splicing lets one gene encode multiple protein isoforms by including or excluding particular exons - one reason humans (~20,000 genes) produce far more than 20,000 proteins.

Translation

Translation assembles a polypeptide from mRNA using transfer RNA (tRNA) and ribosomes (made of rRNA + protein, in two subunits: 30S + 50S = 70S in bacteria; 40S + 60S = 80S in eukaryotes).

Charging the tRNA

Aminoacyl-tRNA synthetases attach the correct amino acid to its tRNA. There is one synthetase per amino acid, and each synthetase recognizes both the amino acid and the tRNA's identity elements (often including the anticodon). Charging consumes ATP. A mischarged tRNA would cause systematic amino-acid substitutions, so this step is critical for fidelity.

The Three Ribosomal Sites

Three Stages

1. Initiation - The small ribosomal subunit, an initiator tRNA carrying methionine (fMet in bacteria), and the mRNA assemble at the start codon AUG. The large subunit then joins to form the complete ribosome with the initiator tRNA in the P site.
2. Elongation - A charged tRNA enters the A site, a peptide bond forms (catalyzed by the peptidyl transferase activity of the 23S/28S rRNA - a ribozyme), and the ribosome translocates by one codon. The deacylated tRNA shifts to the E site and exits.
3. Termination - When a stop codon (UAA, UAG, UGA) enters the A site, release factors bind, hydrolyze the polypeptide from the tRNA, and dissociate the ribosome.

The Genetic Code

The genetic code maps 3-nucleotide codons to amino acids. With 4 bases at 3 positions, there are 4^3 = 64 codons.

• Start codon: AUG (also codes for methionine inside a coding sequence).
• Stop codons: UAA, UAG, UGA (no amino acid; trigger release factors).
• Degeneracy/Redundancy: 61 sense codons encode just 20 amino acids, so most amino acids have multiple codons (leucine, serine, and arginine each have 6).
• Unambiguity: each codon specifies one and only one amino acid.
• Near-universality: the same code is used across bacteria, archaea, and eukaryotes - strong evidence for a common ancestor. (Some mitochondrial codes differ slightly.)

Wobble Hypothesis

Francis Crick's wobble hypothesis explains how about 40 tRNAs can read all 61 sense codons: the third (3') codon position can pair with several bases at the 5' (wobble) position of the anticodon. For example, the inosine modification can pair with U, C, or A. Wobble is why most synonymous codons differ at the third position - silent mutations there are common.

Practice Connection

When the Praxis asks you to predict the effect of a single nucleotide change on the protein, walk through it in order: which strand is the template? Which codon does the new mRNA contain? Does the change hit the third position (likely silent because of wobble), substitute one amino acid (missense), or create a premature stop (nonsense)?